Search for Variation information by Variation ID:
Detailed information for vg0142998716:
| Variant ID: vg0142998716 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42998716 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCGGTCCTCGGGTAGAGTCTTATCTGTGAGGTATGCTTGGATCTCGGCGATCCAAGCAATCAATCTAAGGGAGTTGGGAGCACTCCCCTCGGGTCCCGAG[G/A]
CCTGGACTCCGACGGGCCTCGGGGGCCGATCAGGCGCATCCGTCTCCCCTAAGGGGTCGGGTCGCGCCGACGGCTGGGCAAGCCTTTCTTCAAAGGCGCC
Reverse complement sequence
GGCGCCTTTGAAGAAAGGCTTGCCCAGCCGTCGGCGCGACCCGACCCCTTAGGGGAGACGGATGCGCCTGATCGGCCCCCGAGGCCCGTCGGAGTCCAGG[C/T]
CTCGGGACCCGAGGGGAGTGCTCCCAACTCCCTTAGATTGATTGCTTGGATCGCCGAGATCCAAGCATACCTCACAGATAAGACTCTACCCGAGGACCGC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 6.90% | 0.30% | 1.31% | 91.49% | NA |
| All Indica | 2759 | 0.50% | 0.40% | 1.67% | 97.43% | NA |
| All Japonica | 1512 | 19.80% | 0.10% | 0.40% | 79.63% | NA |
| Aus | 269 | 0.70% | 0.00% | 3.72% | 95.54% | NA |
| Indica I | 595 | 0.50% | 0.30% | 0.00% | 99.16% | NA |
| Indica II | 465 | 0.40% | 0.20% | 0.22% | 99.14% | NA |
| Indica III | 913 | 0.50% | 0.70% | 3.61% | 95.18% | NA |
| Indica Intermediate | 786 | 0.50% | 0.30% | 1.53% | 97.71% | NA |
| Temperate Japonica | 767 | 37.50% | 0.00% | 0.65% | 61.80% | NA |
| Tropical Japonica | 504 | 0.80% | 0.20% | 0.20% | 98.81% | NA |
| Japonica Intermediate | 241 | 3.30% | 0.40% | 0.00% | 96.27% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 12.20% | 0.00% | 0.00% | 87.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0142998716 | G -> A | LOC_Os01g74230.1 | missense_variant ; p.Ala1429Val; MODERATE | nonsynonymous_codon ; A1429V | Average:9.687; most accessible tissue: Zhenshan97 panicle, score: 24.575 | benign  |
0.382 |
DELETERIOUS | 0.01 |
| vg0142998716 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:9.687; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |